Worldwide, over 5 million babies have been born through in vitro fertilization (IVF) since the birth of the first in 1978. Exact numbers are difficult to determine, but it has been estimated that currently 350,000 babies are born yearly through IVF. That number is expected to rise as older maternal age is associated with decreased fertility rates and women in developed countries continue to delay childbirth to later ages. In 95% of IVF procedures, no diagnostic testing of the embryos is performed (wide web at sart.org/find_frm.html). Couples with prior difficulties conceiving or those wishing to avoid the transmission of highly penetrant heritable diseases often choose to perform pre-implantation genetic diagnosis (PGD). PGD involves the biopsy of 1 cell from a 3 day embryo or up to 10 cells at the 5-6 day blastocyst stage followed by genetic analysis. Currently this is either an assay for translocations and the correct chromosome copy number, a unique test designed and validated for each specific heritable disease, or a combination of both. Importantly, none of these approaches can detect de novo mutations or variations that have yet to be associated with a particular disease.
Currently, the only methods available for pre-implantation genetic diagnosis (PGD) of in vitro fertilized embryos are those detecting large genomic alterations or single-gene disorders. These methods can be blind to a large number of potential genomic defects.
While there has been some dispute in the literature regarding the role of IVF in birth defects, two recent studies claim to see an increased incidence in children born through IVF, which could be caused by an excess of genetic defects in these infertile patients. In addition, advanced maternal age has been linked to an increase in aneuploid embryos and advanced paternal age to embryonic de novo mutations. Many recent large scale sequencing studies have found that de novo variations spread across many different genes are likely to be the cause of a large fraction of Autism cases, as well as many other rare congenital disorders. These studies suggest we could be doing more to try to improve the health of IVF newborns.
Current targeted approaches to PGD would miss many important functional changes within the embryonic DNA sequence. Importantly, even a comprehensive WGS-based carrier screen of both parents would not enable targeted pre-implantation or prenatal diagnoses due to de novo mutations. A recent report found that de novo mutations affect functional regions of the genome more often than regions not known to have a function, further underlining the importance of being able to identify this class of genomic variations in PGD. Further, the identification of mutations can useful for a variety of purposes besides for IVF.
Therefore, it is desirable to provide improved techniques for determining mutations in a genome.